I suggest the following steps. (let us know what kind of phantom you have. it will help if we know what you have).
1) Make sure all batteries are maxed (or at least 75%)
2) Calibrate the remote control first.
a) Turn on remote control and plug into PC using USB
b) Open RC assistant and do calibration (be sure to click start and then NEXT). after you have moved all levers around, then click finish.
c) I think you have to do a 2nd calibration for the S1 and S1 switches, do those too.
d) when you are done, click the X at the top of the window to close the RC assistant Window.
e) turn off remote controller.
3) Plug Phantom 2 in USB on PC and turn on (make sure the propellers are removed first).
a) turn on remote controller (this is not connected to PC)
b) open Assistant to calibrate phantom ( not the RC assistant) If you have a Phantom 2, then open the assistant that is ver 3.6.
c) follow steps to calibrate phantom in Basic first. This is where you should be able to see the arrows move from side to side when you move the sticks.
this part makes sure the phantom is getting the signal from the controller.
d) do the next things like IMU...Basic cal, not the Advanced cal and make sure the phantom is level and dont move it while calibrating. this should only take about 15 seconds.
e) close assisant window, unplug USB, then turn off phantom.
4) for test, just take the phantom in your backyard and do compass calibration. then wait for GPS to link up. if that is successful, then try starting motors ( without the propellers).
If it works, then you got it. If not, then let us know and I will try to find a link for you to look at, but we need to know what kind of Phantom you have.